public class PeptideVariantsParameters extends Object implements Serializable
Constructor and Description |
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PeptideVariantsParameters()
Constructor.
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Modifier and Type | Method and Description |
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AaSubstitutionMatrix |
getAaSubstitutionMatrix()
Returns the amino acid substitution matrix to use.
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int |
getnAaDeletions()
Returns the number of amino acid deletions allowed.
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int |
getnAaInsertions()
Returns the number of amino acid insertions allowed.
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int |
getnAaSubstitutions()
Returns the number of amino acid substitutions allowed.
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int |
getnAaSwap()
Returns the number of amino acid swaps allowed.
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static PeptideVariantsParameters |
getNoVariantPreferences()
Returns the preferences corresponding to no variants allowed.
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int |
getnVariants()
Returns the total number of variants allowed.
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String |
getShortDescription()
Returns a short description of the parameters.
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boolean |
getUseSpecificCount()
Returns whether the specific variant count limitations should be used.
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boolean |
isSameAs(PeptideVariantsParameters peptideVariantsPreferences)
Indicates whether another peptide variant preferences is the same as this
one.
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void |
setAaSubstitutionMatrix(AaSubstitutionMatrix aaSubstitutionMatrix)
Sets the amino acid substitution matrix to use.
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void |
setnAaDeletions(int nAaDeletions)
Sets the number of amino acid deletions allowed.
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void |
setnAaInsertions(int nAaInsertions)
Sets the number of amino acid insertions allowed.
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void |
setnAaSubstitutions(int nAaSubstitutions)
Sets the number of amino acid substitutions allowed.
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void |
setnAaSwap(int nAaSwap)
Sets the number of amino acid swaps allowed.
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void |
setnVariants(int nVariants)
Sets the total number of variants allowed.
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void |
setUseSpecificCount(boolean useSpecificCount)
Sets whether the specific variant count limitations should be used.
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public int getnAaDeletions()
public void setnAaDeletions(int nAaDeletions)
nAaDeletions
- the number of amino acid deletions allowedpublic int getnAaInsertions()
public void setnAaInsertions(int nAaInsertions)
nAaInsertions
- the number of amino acid insertions allowedpublic int getnAaSubstitutions()
public void setnAaSubstitutions(int nAaSubstitutions)
nAaSubstitutions
- the number of amino acid substitutions allowedpublic int getnAaSwap()
public void setnAaSwap(int nAaSwap)
nAaSwap
- the number of amino acid swaps allowedpublic AaSubstitutionMatrix getAaSubstitutionMatrix()
public void setAaSubstitutionMatrix(AaSubstitutionMatrix aaSubstitutionMatrix)
aaSubstitutionMatrix
- the amino acid substitution matrix to usepublic boolean getUseSpecificCount()
public void setUseSpecificCount(boolean useSpecificCount)
useSpecificCount
- a boolean indicating whether the specific variant
count limitations should be usedpublic int getnVariants()
public void setnVariants(int nVariants)
nVariants
- the total number of variants allowedpublic boolean isSameAs(PeptideVariantsParameters peptideVariantsPreferences)
peptideVariantsPreferences
- the other preferencespublic String getShortDescription()
public static PeptideVariantsParameters getNoVariantPreferences()
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